Reopening. I'm having quite similar symptoms with 3.1.4 / Linux-x86, so I'm certain this is related.

VBoxManage startvm ... --type gui gets stuck almost every time. It also sleeps waits in futex(). After that, all other VBoxManage commands will also hang; you cannot even start the VirtualBox GUI until you killall all VBoxSVC and VirtualBox processes:
killall -9 VBoxSVC
killall -9 VirtualBox

This is the output of VBoxManage startvm:
Waiting for the remote session to open...
Remote session has been successfully opened.
At this point, it just sits there and waits.

If I start VBoxSVC beforehand, it prints "Informational: VirtualBox object created (rc=NS_OK)." and doesn't do anything else.